IF 2.9 3区生物学

Epigenetics Pub Date : 2025-12-01 Epub Date: 2025-02-25 DOI: 10.1080/15592294.2025.2471129

Allison A Appleton

{"title":"A polyepigenetic glucocorticoid exposure score and HPA axis-related DNA methylation are associated with gestational epigenetic aging.","authors":"Allison A Appleton","doi":"10.1080/15592294.2025.2471129","DOIUrl":"10.1080/15592294.2025.2471129","url":null,"abstract":"Gestational epigenetic aging (GEA) is a novel approach for characterizing associations between prenatal exposures and postnatal risks. Psychosocial adversity in pregnancy may influence GEA, but the molecular mechanisms are not well understood. DNA methylation to glucocorticoid regulation and hypothalamic-pituitary-adrenal (HPA) axis genes are implicated but have not been fully examined in association with GEA. This study investigated whether a polyepigenetic glucocorticoid exposure score (PGES) and HPA axis gene (NR3C1, HSD11B2, FKBP5) methylation were associated with GEA, and whether associations were sex-specific. Participants were from a prospective cohort of racial/ethnic diverse and socially disadvantaged pregnant women and infants (n = 200). DNA methylation variables were estimated using umbilical cord blood. PGES was derived with CpGs shown to be sensitive to synthetic dexamethasone exposure. NR3C1, HSD11B2, and FKBP5 methylation was summarized via factor analysis. We found that PGES (β = -1.12, SE = 0.47, p = 0.02) and several NR3C1 and FKBP5 factor scores were associated with decelerated GEA (all p < 0.05). A significant sex interaction was observed for FKBP5 factor score 3 (β = -0.34, SE = 0.15, p = 0.02) suggesting decelerated GEA for males but not females. This study showed that glucocorticoid regulation-related DNA methylation was associated with a decelerated aging phenotype at birth that might indicate a neonatal risk.","PeriodicalId":11767,"journal":{"name":"Epigenetics","volume":"20 1","pages":"2471129"},"PeriodicalIF":2.9,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11866962/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143499976","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

LncRNA HOTAIR promotes aerobic glycolysis by recruiting Lin28 to induce inflammation and apoptosis in acute lung injury. LncRNA HOTAIR通过募集Lin28诱导急性肺损伤中的炎症和细胞凋亡，促进有氧糖酵解。

IF 3.6 3区生物学

RNA Biology Pub Date : 2025-12-01 Epub Date: 2025-03-07 DOI: 10.1080/15476286.2025.2475255

Junjie Xie, Zhicong Zheng, Bin Wang, Jianfang Zhang, Junqi Jiang, Fengde Wu, Xiangming Zhong, Jianfeng Chen

{"title":"LncRNA HOTAIR promotes aerobic glycolysis by recruiting Lin28 to induce inflammation and apoptosis in acute lung injury.","authors":"Junjie Xie, Zhicong Zheng, Bin Wang, Jianfang Zhang, Junqi Jiang, Fengde Wu, Xiangming Zhong, Jianfeng Chen","doi":"10.1080/15476286.2025.2475255","DOIUrl":"10.1080/15476286.2025.2475255","url":null,"abstract":"Acute lung injury (ALI) is a life-threatening condition with high rates of morbidity and mortality. Recently, there has been growing evidence suggesting a link between lncRNA HOTAIR and ALI. Nonetheless, the precise role and mechanism of lncRNA HOTAIR in ALI remain to be fully elucidated. siHOTAIR transfection, qPCR detection (HOTAIR), ELISA (TNF-α, IL-6, and IL-1β), Lactate detection, Glucose uptake experiment, Cell Apoptosis Analysis, Fluorescence in situ hybridization (FISH) assay. Through siHOTAIR transfection, we discovered that HOTAIR plays a role in the secretion of inflammatory factors in ALI and further regulates glucose uptake and metabolism in lung epithelial cells. Moreover, a comparison between HOTAIR knockdown cells and HOTAIR overexpression cells revealed that HOTAIR promotes cellular aerobic sugar metabolism, leading to increased secretion of inflammatory factors and cell apoptosis. Our in-depth research also identified an interaction between HOTAIR and the LIN28 protein. Knocking down HOTAIR resulted in the downregulation of LIN28 protein expression, which subsequently inhibited the expression of the glucose transporter GLUT1. This indicates that HOTAIR facilitates glucose uptake and boosts cellular aerobic glycolysis by modulating the LIN28 protein, thereby promoting inflammation and apoptosis in acute lung injury. The research findings presented in this article offer significant insights into the function of HOTAIR in ALI and suggest a potential therapeutic target for the treatment of this condition.","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":"22 1","pages":"1-12"},"PeriodicalIF":3.6,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11901367/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143573924","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The LARP6 La module from Tetrabaena socialis reveals structural and functional differences from plant and animal LARP6 homologues. 社会四鳃鱼的LARP6 La模块揭示了植物和动物LARP6同源物在结构和功能上的差异。

IF 3.6 3区生物学

RNA Biology Pub Date : 2025-12-01 Epub Date: 2025-04-09 DOI: 10.1080/15476286.2025.2489303

Emily M Lewis, Olga Becker, Alexis N Symons, Cora LaCoss, A Jasmine Baclig, Avery Guzman, Charles Sanders, Leticia Gonzalez, Lisa R Warner, Karen A Lewis

{"title":"The LARP6 La module from Tetrabaena socialis reveals structural and functional differences from plant and animal LARP6 homologues.","authors":"Emily M Lewis, Olga Becker, Alexis N Symons, Cora LaCoss, A Jasmine Baclig, Avery Guzman, Charles Sanders, Leticia Gonzalez, Lisa R Warner, Karen A Lewis","doi":"10.1080/15476286.2025.2489303","DOIUrl":"10.1080/15476286.2025.2489303","url":null,"abstract":"This study identified the LARP6 La Module from Tetrabaena socialis (T. socialis), a four-celled green algae, in an effort to better understand the evolution of LARP6 structure and RNA-binding activity in multicellular eukaryotes. Using a combination of sequence alignments, domain boundary screens, and structural modelling, we recombinantly expressed and isolated the TsLARP6 La Module to > 98% purity for in vitro biochemical characterization. The La Module is stably folded and exerts minimal RNA binding activity against single-stranded homopolymeric RNAs. Surprisingly, it exhibits low micromolar binding affinity for the vertebrate LARP6 cognate ligand, a bulged-stem loop found in the 5'UTR of collagen type I mRNA, but does not bind double-stranded RNAs of similar size. These result suggests that the TsLARP6 La Module may prefer structured RNA ligands. In contrast, however, the TsLARP6 La Module does not exhibit the RNA chaperone activity that is observed in vertebrate homologs. Therefore, we conclude that protist LARP6 may have both distinct RNA ligands and binding mechanisms from the previously characterized LARP6 proteins of animals and vascular plants, thus establishing a distinct third class of the LARP6 protein family.","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":" ","pages":"1-9"},"PeriodicalIF":3.6,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11988235/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143780999","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

CEACAM5 exacerbates asthma by inducing ferroptosis and autophagy in airway epithelial cells through the JAK/STAT6-dependent pathway. CEACAM5通过JAK/ stat6依赖通路诱导气道上皮细胞铁凋亡和自噬，从而加重哮喘。

IF 5.2 2区生物学

Redox Report Pub Date : 2025-12-01 Epub Date: 2025-01-23 DOI: 10.1080/13510002.2024.2444755

Si Liu, Li Chen, Yunxiao Shang

{"title":"CEACAM5 exacerbates asthma by inducing ferroptosis and autophagy in airway epithelial cells through the JAK/STAT6-dependent pathway.","authors":"Si Liu, Li Chen, Yunxiao Shang","doi":"10.1080/13510002.2024.2444755","DOIUrl":"10.1080/13510002.2024.2444755","url":null,"abstract":"Objectives: Asthma, a prevalent chronic disease, poses significant health threats and burdens healthcare systems. This study focused on the role of bronchial epithelial cells in asthma pathophysiology.Methods: Bioinformatics was used to identify key asthmarelated genes. An ovalbumin-sensitized mouse model and an IL-13-stimulated Beas-2B cell model were established for further investigation.Results: Carcinoembryonic antigen-related cell adhesion molecule 5 (CEACAM5) was identified as a crucial gene in asthma. CEACAM5 expression was elevated in asthmatic mouse lung tissues and IL-13-stimulated Beas-2B cells, primarily in bronchial epithelial cells. CEACAM5 induced reactive oxygen species (ROS), lipid peroxidation, and ferroptosis. Interfering with CEACAM5 reduced ROS, malondialdehyde levels, and enhanced antioxidant capacity, while inhibiting iron accumulation and autophagy. Overexpression of CEACAM5 in IL-13-stimulated cells activated the JAK/STAT6 pathway, which was necessary for CEACAM5-induced autophagy, ROS accumulation, lipid peroxidation, and ferroptosis.Conclusion: CEACAM5 promotes ferroptosis and autophagy in airway epithelial cells via the JAK/STAT6 pathway, exacerbating asthma symptoms. It represents a potential target for clinical treatment.","PeriodicalId":21096,"journal":{"name":"Redox Report","volume":"30 1","pages":"2444755"},"PeriodicalIF":5.2,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11758806/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143059975","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

6S-1 pRNA 9-mers are a prominent length species during outgrowth of Bacillus subtilis cells from extended stationary phase. S-1 pRNA 9-mers是枯草芽孢杆菌延长固定期生长过程中的一个突出的长度物种。

IF 3.6 3区生物学

RNA Biology Pub Date : 2025-12-01 Epub Date: 2025-04-14 DOI: 10.1080/15476286.2025.2484519

Katrin Damm, Paul Klemm, Marcus Lechner, Dominik Helmecke, Roland K Hartmann

{"title":"6S-1 pRNA 9-mers are a prominent length species during outgrowth of Bacillus subtilis cells from extended stationary phase.","authors":"Katrin Damm, Paul Klemm, Marcus Lechner, Dominik Helmecke, Roland K Hartmann","doi":"10.1080/15476286.2025.2484519","DOIUrl":"10.1080/15476286.2025.2484519","url":null,"abstract":"Bacterial RNA polymerases (RNAP) utilize 6S RNAs as templates to synthesize ultrashort transcripts (up to ~14 nt), termed product RNAs (pRNAs), that play a key role in reversing the blockage of RNAP by 6S RNA. Here, we resolved the pRNA length profile of 6S-1 RNA from B. subtilis, a major model system for the study of 6S RNA biology, during outgrowth of cells from extended stationary phase. 9-mers were found to be a particularly abundant pRNA length species, followed by 8-/10-/11-mers and 13-/14-mers. Consistent with in vitro data from the Escherichia coli system, these findings support the mechanistic model according to which the housekeeping sigma factor (σ70 or σA) dissociates from 6S RNA:RNAP complexes upon synthesis of pRNA 9-mers, followed by final dissociation of 6S RNA and RNAP upon synthesis of longer pRNAs (13-/14-mers). Methodologically, the identification of such ultrashort RNAs in total cellular extracts by RNA-Seq is inefficient with standard protocols using adapter ligation to RNA 3'-ends for reverse transcription and PCR-based cDNA sequencing. Here, we demonstrate that ultrashort RNAs can instead be incorporated into RNA-Seq libraries by polyA-, polyC- and potentially also polyU-tailing of their 3'-ends. At positions where a non-tailing nucleotide is followed by one or more tailing nucleotides, an algorithm that integrates RNA-Seq results from at least two different 3'-end tailings allows one to approximate the fraction of read counts at such ambiguous positions. Finally, methodological biases and potential applications of our approach to other short RNAs are discussed.","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":" ","pages":"1-14"},"PeriodicalIF":3.6,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12005410/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143710720","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Antibody-dependent enhancement of ORFV uptake into host cells. 抗体依赖性增强ORFV进入宿主细胞的摄取。

IF 5.5 1区农林科学

Virulence Pub Date : 2025-12-01 Epub Date: 2025-02-15 DOI: 10.1080/21505594.2025.2466503

Xidian Tang, Chenyibo Zhang, Qingru Geng, Dekun Chen, Wentao Ma

{"title":"Antibody-dependent enhancement of ORFV uptake into host cells.","authors":"Xidian Tang, Chenyibo Zhang, Qingru Geng, Dekun Chen, Wentao Ma","doi":"10.1080/21505594.2025.2466503","DOIUrl":"10.1080/21505594.2025.2466503","url":null,"abstract":"Orf virus (ORFV) has been demonstrated to infect both goat non-immune cells, specifically goat epithelial cells, and goat blood immune cells. Our previous studies have indicated that ORFV gains entry into goat epithelial cells via clathrin-mediated endocytosis and macropinocytosis pathways. However, the pathway by which ORFV enters goat blood immune cells has not yet been elucidated. Our findings revealed a differential viral internalization pathway in ORFV-infects goat immune cells contrasting the internalization pathways in goat epithelial cells, potentially involving an antibody-related mechanism. Therefore, our hypothesis posits that ORFV gains entry into goat immune cells via the antibody-dependent enhancement (ADE) pathway. Our experimental findings confirm the presence of the ADE effect in ORFV-infected goat immune cells, mediated by Fc receptors (FcRs) as demonstrated in antibody-blocking experiments. Furthermore, the ADE effect was also observed in goat epithelial cells. Nevertheless, the ADE effect observed in goat epithelial cells was not found to be dependent on the interaction between the virus-antibody complex and Fc receptors, as demonstrated by antibody-blocking experiments. Instead, it is suggested that an alternative mechanism involving the complement factor and complement receptors (CRs) may be responsible. Overall, this research offers insights into the unique ADE pathway of ORFV infection in different cell types, offering a novel perspective on the infection and pathogenic mechanisms of ORFV.","PeriodicalId":23747,"journal":{"name":"Virulence","volume":"16 1","pages":"2466503"},"PeriodicalIF":5.5,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11834454/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143426363","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Non-invasive electron paramagnetic resonance imaging detects tumor redox imbalance induced by ferroptosis. 无创电子顺磁共振成像检测由铁下垂引起的肿瘤氧化还原失衡。

IF 5.2 2区生物学

Redox Report Pub Date : 2025-12-01 Epub Date: 2025-01-21 DOI: 10.1080/13510002.2025.2454887

Kazuhiro Kato, Hironobu Yasui, Hideo Sato-Akaba, Miho C Emoto, Hirotada G Fujii, Maciej M Kmiec, Periannan Kuppusamy, Masaki Nagane, Tadashi Yamashita, Osamu Inanami

{"title":"Non-invasive electron paramagnetic resonance imaging detects tumor redox imbalance induced by ferroptosis.","authors":"Kazuhiro Kato, Hironobu Yasui, Hideo Sato-Akaba, Miho C Emoto, Hirotada G Fujii, Maciej M Kmiec, Periannan Kuppusamy, Masaki Nagane, Tadashi Yamashita, Osamu Inanami","doi":"10.1080/13510002.2025.2454887","DOIUrl":"10.1080/13510002.2025.2454887","url":null,"abstract":"Targeting ferroptosis, cell death caused by the iron-dependent accumulation of lipid peroxides, and disruption of the redox balance are promising strategies in cancer therapy owing to the physiological characteristics of cancer cells. However, the detection of ferroptosis using in vivo imaging remains challenging. We previously reported that redox maps showing the reduction power per unit time of implanted tumor tissues via non-invasive redox imaging using a novel, compact, and portable electron paramagnetic resonance imaging (EPRI) device could be compared with tumor tissue sections. This study aimed to apply the EPRI technique to the in vivo detection of ferroptosis. Notably, redox maps reflecting changes in the redox status of tumors induced by the ferroptosis-inducing agent imidazole ketone erastin (IKE) were compared with the immunohistochemical images of 4-hydroxynonenal (4-HNE) in tumor tissue sections. Our comparison revealed a negative correlation between the reducing power of tumor tissue and the number of 4-HNE-positive cells. Furthermore, the control and IKE-treated groups exhibited significantly different distributions on the correlation map. Therefore, redox imaging using EPRI may contribute to the non-invasive detection of ferroptosis in vivo.","PeriodicalId":21096,"journal":{"name":"Redox Report","volume":"30 1","pages":"2454887"},"PeriodicalIF":5.2,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11753017/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143010806","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

AUGcontext DB: a comprehensive catalog of the mRNA AUG initiator codon context across eukaryotes. AUGcontext DB：真核生物中mRNA AUG启动子密码子上下文的综合目录。

IF 3.6 3区生物学

RNA Biology Pub Date : 2025-12-01 Epub Date: 2025-02-13 DOI: 10.1080/15476286.2025.2465196

Vincent G Osnaya, Laura Gómez-Romero, Gabriel Moreno-Hagelsieb, Greco Hernández

{"title":"AUGcontext DB: a comprehensive catalog of the mRNA AUG initiator codon context across eukaryotes.","authors":"Vincent G Osnaya, Laura Gómez-Romero, Gabriel Moreno-Hagelsieb, Greco Hernández","doi":"10.1080/15476286.2025.2465196","DOIUrl":"10.1080/15476286.2025.2465196","url":null,"abstract":"The mRNA translation defines the composition of the cell proteome in all forms of life and diseases. In this process, precise selection of the mRNA translation initiation site (TIS) is crucial, as it establishes the correct open reading frame for triplet decoding. We have gathered and curated all published TIS consensus context sequences. We also included the TIS consensus context from novel 538 fungal genomes available from NCBI's RefSeq database. To do so, we wrote ad hoc programs in PERL to find and extract the TIS for each annotated gene, plus ten bases upstream and three downstream. For each genome, the sequences around the TIS of each gene were obtained, and the consensus was further calculated according to the Cavener rules and by the LOGOS algorithm. We created AUGcontext DB, a portal with a comprehensive collection of TIS context sequences across eukaryotes in a range from -10 to + 6. The compilation covers species of 30 vertebrates, 17 invertebrates, 25 plants, 14 fungi, and 11 protists studied in silico; 23 experimental studies; data on biotechnology; and the discovery of 8 diseases associated with specific mutations. Additionally, TIS context sequences of cellular IRESs were included. AUGcontext DB belongs to the National Institute of Cancer (Instituto Nacional de Cancerología, INCan), Mexico, and is freely available at http://108.161.138.77:8096/. Our catalogue allows us to do comparative studies between species, may help improve the diagnosis of certain diseases, and will be key to maximize the production of recombinant proteins.","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":" ","pages":"1-5"},"PeriodicalIF":3.6,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11834415/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143399899","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Virulence factors and therapeutic methods of Trueperella pyogenes: A review. 化脓性true eperella的毒力因素及治疗方法综述。

IF 5.5 1区农林科学

Virulence Pub Date : 2025-12-01 Epub Date: 2025-02-21 DOI: 10.1080/21505594.2025.2467161

Xiangfu Wen, Jia Cheng, Mingchao Liu

引用次数: 0

Insights and progress on epidemic characteristics, pathogenesis, and preventive measures of African swine fever virus: A review. 非洲猪瘟病毒流行特征、发病机制和预防措施的研究进展

IF 5.5 1区农林科学

Virulence Pub Date : 2025-12-01 Epub Date: 2025-03-06 DOI: 10.1080/21505594.2025.2457949

Mei Li, Haixue Zheng

引用次数: 0

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